Butler Marguerite A, King Aaron A
Am Nat. 2004 Dec;164(6):683-695. doi: 10.1086/426002.
Biologists employ phylogenetic comparative methods to study adaptive evolution. However, none of the popular methods model selection directly. We explain and develop a method based on the Ornstein-Uhlenbeck (OU) process, first proposed by Hansen. Ornstein-Uhlenbeck models incorporate both selection and drift and are thus qualitatively different from, and more general than, pure drift models based on Brownian motion. Most importantly, OU models possess selective optima that formalize the notion of adaptive zone. In this article, we develop the method for one quantitative character, discuss interpretations of its parameters, and provide code implementing the method. Our approach allows us to translate hypotheses regarding adaptation in different selective regimes into explicit models, to test the models against data using maximum-likelihood-based model selection techniques, and to infer details of the evolutionary process. We illustrate the method using two worked examples. Relative to existing approaches, the direct modeling approach we demonstrate allows one to explore more detailed hypotheses and to utilize more of the information content of comparative data sets than existing methods. Moreover, the use of a model selection framework to simultaneously compare a variety of hypotheses advances our ability to assess alternative evolutionary explanations.
生物学家运用系统发育比较方法来研究适应性进化。然而，现有的主流方法都没有直接对选择进行建模。我们解释并拓展了一种基于奥恩斯坦 - 乌伦贝克（OU）过程的方法，该方法最初由汉森提出。奥恩斯坦 - 乌伦贝克模型同时纳入了选择和漂变，因此在性质上不同于基于布朗运动的纯漂变模型，且更为通用。最重要的是，OU模型拥有选择性最优值，这些最优值使适应区的概念形式化。在本文中，我们针对一个数量性状拓展了该方法，讨论了其参数的解释，并提供了实现该方法的代码。我们的方法使我们能够将关于不同选择机制下适应的假设转化为明确的模型，使用基于最大似然的模型选择技术针对数据检验这些模型，并推断进化过程的细节。我们用两个实例来说明该方法。相对于现有方法，我们展示的直接建模方法使人们能够探索更详细的假设，并比现有方法更多地利用比较数据集的信息内容。此外，使用模型选择框架同时比较各种假设提高了我们评估替代性进化解释的能力。
